load_plink_ld: Load a plink LD file

In nwvankuren/genomics-plotting: Utilities for plotting statistics from genome-wide analyses

Description

This function loads a file containing pairwise LD estimates generated by plink. A typical command to generate this file would be: plink –bfile input –allow-extra-chr –r2 inter-chr gz \ –ld-window-r2 0.0 –out test.plink –chr scaffold_1000 This will only keep SNPs on the same chromosome, because it assumes that you do not know the distance between different scaffolds, even those located to the same chromosome according to reordering information.

Usage

load_plink_ld(file, max_dist = 50000, keep_ids = FALSE,
  stat = c("r2", "dp"))

Arguments

file	Name of a file containing LD values calculated using
max_dist	Maximum allowed distance between two SNPs, in bp
keep_ids	Keep SNP IDs in returned tibble? T / F
stat	Which statistic to keep? r2, d, and/or dp (D' and D'-signed)

Value

A tibble with pairwise LD measures

Examples

a <- system.file("extdata", "test.plink.ld.gz", package = "gwplotting" )
b <- load_plink_ld( a )
b

nwvankuren/genomics-plotting documentation built on April 14, 2021, 1:18 a.m.